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Yorodumi- PDB-4z4z: Crystal structure of GII.10 P domain in complex with 30mM B antig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z4z | |||||||||
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Title | Crystal structure of GII.10 P domain in complex with 30mM B antigen (trisaccharide) | |||||||||
Components | Capsid protein | |||||||||
Keywords | VIRAL PROTEIN / HBGA / norovirus / protruding domain | |||||||||
Function / homology | Function and homology information Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | Norwalk virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | |||||||||
Authors | Leuthold, M.M. / Koromyslova, A.D. / Hansman, G.S. | |||||||||
Citation | Journal: Virology / Year: 2015 Title: The sweet quartet: Binding of fucose to the norovirus capsid. Authors: Koromyslova, A.D. / Leuthold, M.M. / Bowler, M.W. / Hansman, G.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z4z.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z4z.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 4z4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/4z4z ftp://data.pdbj.org/pub/pdb/validation_reports/z4/4z4z | HTTPS FTP |
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-Related structure data
Related structure data | 4z4rC 4z4sC 4z4tC 4z4uC 4z4vC 4z4wC 4z4yC 3onuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: MET / End label comp-ID: MET
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-Components
#1: Protein | Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: residues 224-538 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norwalk virus / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F4T5 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium nitrate, bis-tris propane, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.984463 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 20, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984463 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.86 Å / Num. obs: 65787 / % possible obs: 98.88 % / Redundancy: 3 % / Rmerge(I) obs: 0.06859 / Net I/σ(I): 11.57 |
Reflection shell | Resolution: 1.801→1.865 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.14 / Num. unique all: 6308 / % possible all: 95.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ONU Resolution: 1.801→42.86 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.69 Å2 / Biso mean: 22.3354 Å2 / Biso min: 9.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→42.86 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
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